[gmx-users] npt equilbration + density

Bahar Mehrpuyan baharmehrpuyan at yahoo.com
Fri Feb 8 17:54:58 CET 2013

Thanks Justin for the reply.

 i use SPC water model (12000 molecules). in literature there are 
different values for density which depend simulation time, number of 
water molecules , etc. (for example this paper : 

 From: Justin Lemkul <jalemkul at vt.edu>
To: Bahar Mehrpuyan <baharmehrpuyan at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, February 8, 2013 7:56 PM
Subject: Re: [gmx-users] npt equilbration + density

On 2/8/13 10:49 AM, Bahar Mehrpuyan wrote:
> Dear gmx users
> My system is a single amino acid in water. I use two stage equilibration :  NVT (300 k) and NPT (300k , 1 barr) with position restrain.
> NPT simulation were done for 2.4 ns and 1.14 barr was obtained for pressure.
> but density is 974.031 . is this reasonable?

That depends on the water model you use and what its expected density is.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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